<!-- DTD for toppred output   -->
<!ELEMENT  toppreds (parameters?, toppred+)>

<!ELEMENT toppred  (parameters?, sequence?, annotation?, plot?, tmsummary, topologies?)>

<!-- parameters of the toppred algorithm -->
<!ELEMENT  parameters   (corewindow, wedgewindow, certain, putative, distsegments, looplength, eucaryotes, hydrophobycity)>

<!ELEMENT corewindow (#PCDATA)>
<!ATTLIST corewindow
        default (true|false) "false">
<!ELEMENT wedgewindow (#PCDATA)>
<!ATTLIST wedgewindow
        default (true|false) "false">
<!ELEMENT certain (#PCDATA)>
<!ATTLIST certain
        default (true|false) "false">
<!ELEMENT putative (#PCDATA)>
<!ATTLIST putative
        default (true|false) "false">  
<!ELEMENT distsegments (#PCDATA)>
<!ATTLIST distsegments
        default (true|false) "false">
<!ELEMENT looplength (#PCDATA)>
<!ATTLIST distsegments
        default (true|false) "false">
<!ELEMENT kingdom (#PCDATA)>
<!ATTLIST kingdom
        default (true|false) "false">
<!ELEMENT hydrophobycity (#PCDATA)>
<!ATTLIST hydrophobycity
        default (true|false) "false">

<!-- programme results -->
<!ELEMENT  results (sequence)+>


<!ATTLIST sequence
        id  ID    #IMPLIED
        len CDATA #IMPLIED>

<!ELEMENT annotation (#PCDATA)>

<!ELEMENT plot EMPTY>
<!ATTLIST plot
        hydro CDATA  #REQUIRED
        gplot CDATA  #IMPLIED>

<!ELEMENT tmsummary (segment*)>
<!ATTLIST tmsummary
        segments  CDATA "0">
        

<!ELEMENT segment EMPTY>
<!ATTLIST segment 
        start CDATA  #REQUIRED 
        stop  CDATA  #IMPLIED
        hp    CDATA  #REQUIRED
        type  (putative|certain) "certain">

<!ELEMENT topologies (toppology+)>
<!ATTLIST topologies
        maxtopos  CDATA #IMPLIED
        topoprint CDATA #IMPLIED>

<!ELEMENT topology (loop?, (transmem, loop)+, transmem?)>
<!ATTLIST topology 
        nr       ID     #IMPLIED
        prob     CDATA  #IMPLIED
        darglys  CDATA  #REQUIRED
        dcytext  CDATA  #IMPLIED
        dncharge CDATA  #IMPLIED
        dnnegpos CDATA  #IMPLIED
        image    CDATA  #IMPLIED
        orient   CDATA  #IMPLIED>

<!ELEMENT transmem EMPTY>
<!ATTLIST transmem
        start CDATA  #REQUIRED
        stop  CDATA  #IMPLIED
        prob  CDATA  #IMPLIED
        hp    CDATA  #REQUIRED>

<!ELEMENT loop EMPTY>
<!ATTLIST loop  
        type (ext|cyt|unknown) "unknown"    
        start   CDATA  #REQUIRED
        stop    CDATA  #IMPLIED
        darglys CDATA  #REQUIRED
        dcytext CDATA  #IMPLIED
        decisive (darglys|dcytext) "darglys">










